Expansion and transformation of the minor spliceosomal system in the slime mold Physarum polycephalum

Abstract

Spliceosomal introns interrupt nuclear genes and are removed from RNA transcripts ("spliced") by machinery called spliceosomes. Although the vast majority of spliceosomal introns are removed by the so-called major (or "U2") spliceosome, diverse eukaryotes also contain a rare second form, the minor ("U12") spliceosome, and associated ("U12-type") introns.^1-3 In all characterized species, U12-type introns are distinguished by several features, including being rare in the genome (∼0.5% of all introns),^4-6 containing extended evolutionarily conserved splicing motifs,^4,5,7,8 being generally ancient,^9,10 and being inefficiently spliced.^11-13 Here, we report a remarkable exception in the slime mold Physarum polycephalum. The P. polycephalum genome contains >20,000 U12-type introns-25 times more than any other species-enriched in a diversity of non-canonical splice boundaries as well as transformed splicing signals that appear to have co-evolved with the spliceosome due to massive gain of efficiently spliced U12-type introns. These results reveal an unappreciated dynamism of minor spliceosomal introns and spliceosomal introns in general.

Keywords: U12; U12-type introns; bioinformatics; comparative genomics; evolution; genomics; intron evolution; intron gain; minor introns; minor spliceosome.